Can I go back to change the fact that my wife did have income and we are eligible for the two income marriage deduction?

on a joint return, all taxable income of both spouses must be reported. if you already filed and it was accepted, you must wait until the return is fully processed and then amend it. if you haven't filed you can correct it now before filing.  

Did you e-file already?   If you have already e-filed, you will have to wait until the return has been fully processed and then amend to add your spouse's retirement income.   

Your joint return is supposed to have ALL of your combined income ---income from working , pension income, Social Security, IRA or 401k distributions, etc. etc. etc.---not just income from working.

If you have not yet e-filed then go back to your federal return and add any income your spouse received.  It will flow to the state return.

Go to Federal> Wages & Income>>Retirement Plans and Social Security  (SSA1099 and 1099RRB) to enter your SSA1099.

To enter your retirement income, Go to  Federal> Wages and Income>Retirement Plans and Social Security>IRA  401 k) Pension Plan Withdrawals to enter your 1099R.